4FCO

Crystal structure of bace1 with its inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4FCO/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-05-25 Released: 2013-05-29 
• Deposition Author(s): Chen, T.T., Chen, W.Y., Li, L., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.183 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations

Xu, Y.C., Chen, W.Y., Chen, T.T., Li, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.37 kDa 
• Atom Count: 3,437 
• Modelled Residue Count: 374 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	433	Homo sapiens	Mutation(s): 2  Gene Names: BACE, BACE1, KIAA1149 EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0U4	E [auth A]	N-[(2S,3R)-4-{[2-(1-benzylpiperidin-4-yl)ethyl]amino}-3-hydroxy-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide C42 H53 N5 O5 S IMNAYTZSJCRZIO-RLRCJDGOSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
URE	F [auth A], G [auth A]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0U4	BindingDB:  4FCO	IC50: min: 99, max: 567 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.183 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.44	α = 90
b = 128.42	β = 90
c = 76.27	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Chen, T.T., Chen, W.Y., Li, L., Xu, Y.C.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release